From 24ee2349c16f159f2627665938fd76d599055a9a Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Thu, 22 Nov 2018 10:43:54 +1100 Subject: gridss: fix configure file optional string error --- tools/gridss-softClipsToSplitReads.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'tools/gridss-softClipsToSplitReads.nix') diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index 5fce894..1f9c8b4 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -34,8 +34,8 @@ stdenv.mkDerivation rec { I=${input} \ O=$out \ ${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \ - ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ + ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ WORKER_THREADS=$NIX_BUILD_CORES ''; - passthru.filetype = filetype.bam { ref = ref; sort = sorting.none {}; } + passthru.filetype = filetype.bam { ref = ref; sorting = matchFileSorting "grids-softClipsToSplitReads" { coord = _: input.sorting; name = _: sort.none {}; none = _: input.sorting;} input;}; } -- cgit v1.2.3 From 0ade062d2da8a7111b14aa3d72ef7c741e98352d Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Thu, 22 Nov 2018 10:44:31 +1100 Subject: gridss: restructure gridss pipeline --- tools/gridss-softClipsToSplitReads.nix | 2 -- 1 file changed, 2 deletions(-) (limited to 'tools/gridss-softClipsToSplitReads.nix') diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index 1f9c8b4..2fff15c 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -17,8 +17,6 @@ let ref = matchFiletype "gridss-softClipsToSplitReads" { bam = x: x.ref; } input; in -assert (matchFileSorting "gridss-softClipsToSplitReads" { name = _: true; } input); - stdenv.mkDerivation rec { name = "gridss-softClipsToSplitReads"; buildInputs = [ jre bwa ]; -- cgit v1.2.3